X-103323975-T-G

Variant names:

• chrX-103323975-T-G
• rs5987515

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.67 (18708 hom., 21540 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185
• Publications: 3 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.670 AC: 73960 AN: 110382 Hom.: 18704 Cov.: 22

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.645

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.670 AC: 74015 AN: 110439 Hom.: 18708 Cov.: 22 AF XY: 0.659 AC XY: 21540 AN XY: 32683

African (AFR) AF: 0.910 AC: 27678 AN: 30399

American (AMR) AF: 0.618 AC: 6442 AN: 10432

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 1751 AN: 2629

East Asian (EAS) AF: 0.591 AC: 2044 AN: 3461

South Asian (SAS) AF: 0.736 AC: 1863 AN: 2530

European-Finnish (FIN) AF: 0.467 AC: 2735 AN: 5855

Middle Eastern (MID) AF: 0.544 AC: 117 AN: 215

European-Non Finnish (NFE) AF: 0.572 AC: 30166 AN: 52733

Other (OTH) AF: 0.645 AC: 972 AN: 1508

Alfa AF: 0.478 Hom.: 2661

Bravo AF: 0.691

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.73
PhyloP100		0.18

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs5987515; hg19: chrX-102578903;